Bio::DB::Ace(3pm)

💖 Bio::DB::Ace 💖

okay bestie, so this is Bio::DB::Ace — it's the User Contributed Perl Documentation page for a Perl module that gives you a database object interface to ACeDB servers. it's serving database-access realness and honestly? iconic. 🧬✨

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✨ NAME ✨

Bio::DB::Ace — Database object interface to ACeDB servers 🦋

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🌸 SYNOPSIS 🌸

here's the vibe, look:

$db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');

$seq = $db->get_Seq_by_id('J00522'); # Unique ID

# or ...

$seq = $db->get_Seq_by_acc('J00522'); # Accession Number

like, you make a $db, you ask it for a sequence. that's it. that's the whole thing. slay. 💅

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💜 DESCRIPTION 💜

so what this does is give you a standard BioPerl database access to Ace, built on top of Lincoln Steins's absolutely legendary AcePerl module. no cap.

⚠️ but listen — you need to download and install the aceperl module from

http://stein.cshl.org/AcePerl/

before this interface will work. fr fr. it will not work without it. 😭

and rn, this interface is designed to work through an aceclient/aceserver type mechanism. that's the whole design. that's the assignment. 🎀

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🌈 INSTALLING ACEPERL 🌈

okay so first things first, go download the latest aceperl tar file, then gunzip/untar it and cd into the directory. it's a standard CPAN-style directory, so if you go

Perl Makefile.PL
make
<become root>
make install

then boom — Aceperl is installed. you ate that. 🍓

and if you wanna install it somewhere else, just use the PREFIX mechanism. flexible queen behavior. 👑

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💬 FEEDBACK 💬

📬 Mailing Lists 📬

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. so send your comments and suggestions — preferably to one of the Bioperl mailing lists. your participation is much appreciated, and I mean that so sincerely. 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support 🫂

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. the reason is that there are many experienced and responsive experts who will be able to look at the problem and quickly address it. it's giving "ask the group chat, not just one person." 💖

and if you can, please include a thorough description of the problem with code and data examples. help us help you bestie. 🙏

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

no gatekeeping, just file it. 🔥

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👑 AUTHOR - Ewan Birney 👑

email: birney@ebi.ac.uk

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's the lil tell, iykyk. 🤫

⭐ get_Seq_by_id ⭐

Title   : get_Seq_by_id
Usage   : $seq = $db->get_Seq_by_id($uid);
Function: Gets a Bio::Seq object by its unique identifier/name
Returns : a Bio::Seq object
Args    : $id : the id (as a string) of the desired sequence entry

⭐ get_Seq_by_acc ⭐

Title   : get_Seq_by_acc
Usage   : $seq = $db->get_Seq_by_acc($acc);
Function: Gets a Bio::Seq object by its accession number
Returns : a Bio::Seq object
Args    : $acc : the accession number of the desired sequence entry

⭐ _aceobj ⭐

Title   : _aceobj
Usage   : $ace = $db->_aceobj();
Function: Get/Set on the acedb object
Returns : Ace object
Args    : New value of the ace object

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and that's the whole page, bestie!! 💜 this lil writeup was brought to you by perl v5.30.0, dated 2019-11-25, and it lives under the name Bio::DB::Ace(3pm). go forth and query your ACeDB servers, you absolute main character. 💅✨🦋🎀